Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level

Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes

Comparison of the ratio of nonsynonymous to synonymous polymorphisms within species with the ratio of nonsynonymous to synonymous substitutions between species has been widely used as a supposed indicator of positive Darwinian selection, with the ratio of these 2 ratios being designated as a neutrality index (NI). Comparison of genome-wide polymorphism within 12 species of bacteria with divergence from an outgroup species showed substantial differences in NI among taxa. A low level of nonsynonymous polymorphism at a locus was the best predictor of NI < 1, rather than a high level of nonsynonymous substitution between species. Moreover, genes with NI < 1 showed a strong tendency toward the occurrence of rare nonsynonymous polymorphisms, as expected under the action of ongoing purifying selection. Thus, our results are more consistent with the hypothesis that a high relative rate of between-species nonsynonymous substitution reflects mainly the action of purifying selection within species to eliminate slightly deleterious mutations rather than positive selection between species. This conclusion is consistent with previous results highlighting an important role of slightly deleterious variants in bacterial evolution and suggests caution in the use of the McDonald-Kreitman test and related statistics as tests of positive selection.

Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex

Paracoccidioides brasiliensis is a dimorphic fungus that is the causative agent of paracoccidioidomycosis, the most important prevalent systemic mycosis in Latin America. Recently, the existence of three genetically isolated groups in P. brasiliensis was demonstrated, enabling comparative studies of molecular evolution among P. brasiliensis lineages. Thirty-two gene sequences coding for putative virulence factors were analyzed to determine whether they were under positive selection. Our maximum likelihood–based approach yielded evidence for selection in 12 genes that are involved in different cellular processes. An in-depth analysis of four of these genes showed them to be either antigenic or involved in pathogenesis. Here, we present evidence indicating that several replacement mutations in gp43 are under positive balancing selection. The other three genes (fks, cdc42 and p27) show very little variation among the P. brasiliensis lineages and appear to be under positive directional selection. Our results are consistent with the more general observations that selective constraints are variable across the genome, and that even in the genes under positive selection, only a few sites are altered. We present our results within an evolutionary framework that may be applicable for studying adaptation and pathogenesis in P. brasiliensis and other pathogenic fungi.

The fungus Paracoccidioides brasiliensis is the causative agent of paracoccidioidomycosis, a severe pulmonary mycosis that is endemic to Latin America, where an estimated 10 million people are infected with the fungus. Despite the importance of this disease, we know little about the ecological and evolutionary history of this fungus. Here, we present a survey of genetic variation in putative virulence genes in P. brasiliensis in what constitutes the first systematic approach to understand the molecular evolution of the fungus. We used a population genetics approach to determine the role has natural selection played in the coding genes for proteins involved in pathogenesis. We found that nonsynonymous mutations are more common in genes that code for virulence factors than in housekeeping genes. Our results suggest that positive selection has played an important role in the evolution of virulence factors of P. brasiliensis and is therefore an important factor in the host–pathogen dynamics. Our results also have implications for the possible development of a vaccine against paracoccidioidomycosis, since gp43—the main vaccine candidate—has a high level of polymorphism maintained by natural selection.

Searching for candidate speciation genes using a proteomic approach: seminal proteins in field crickets

In many animals, male seminal proteins influence gamete interactions and fertilization ability and are probably involved in barriers to gene flow between diverging lineages. Here we use a proteomic approach to identify seminal proteins that are transferred to females during copulation and that may be involved in fertilization barriers between two hybridizing field crickets (Gryllus firmus and Gryllus pennsylvanicus). Analyses of patterns of divergence suggest that much of the field cricket genome has remained undifferentiated following the evolution of reproductive isolation. By contrast, seminal protein genes are highly differentiated. Tests of selection reveal that positive selection is likely to be responsible for patterns of differentiation. Together, our observations suggest that some of the loci encoding seminal proteins may indeed play a role in fertilization barriers in field crickets.

Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures

Analysis of complete polyprotein-encoding sequences of hepatitis C virus genotype 1b (HCV-1b) showed evidence not only of past purifying selection but also of abundant slightly deleterious non-synonymous variants subject to ongoing purifying selection. The NS3 protein (with protease and NTPase/helicase activity) revealed less evidence of purifying selection acting on the cytotoxic T cells (CTL) epitopes than did the other proteins, whereas outside the CTL epitopes NS3 was more conserved than the other proteins. Moreover, NS3 showed a high incidence of forward-and-backward or parallel non-synonymous changes in CTL epitopes, as measured by the consistency index across the phylogeny of HCV-1b genomes computed at non-singleton non-synonymous polymorphic sites. This result implies that certain non-synonymous mutations have recurred frequently throughout the phylogeny in the codons encoding the epitopes in NS3. This pattern is most easily explained by the frequent re-occurrence of the same set of escape mutations in CTL epitopes of NS3, which are selectively favoured within hosts expressing the presenting class I major histocompatibility complex molecule, but are subject to purifying selection at the population level. The fact that this pattern is most strikingly observed in the case of NS3 suggests that the evolutionary conflict between immune escape and functional constraint on the protein is more acute in the case of NS3 than any of the other proteins of HCV-1b.

Near neutrality: leading edge of the neutral theory of molecular evolution

The nearly neutral theory represents a development of Kimura's neutral theory of molecular evolution that makes testable predictions that go beyond a mere null model. Recent evidence has strongly supported several of these predictions, including the prediction that slightly deleterious variants will accumulate in a species that has undergone a severe bottleneck or in cases where recombination is reduced or absent. Because bottlenecks often occur in speciation and slightly deleterious mutations in coding regions will usually be nonsynonymous, we should expect that the ratio of nonsynonymous to synonymous fixed differences between species should often exceed the ratio of nonsynonymous to synonymous polymorphisms within species. Many data support this prediction, although they have often been wrongly interpreted as evidence for positive Darwinian selection. The use of conceptually flawed tests for positive selection has become widespread in recent years, seriously harming the quest for an understanding of genome evolution. When properly analyzed, many (probably most) claimed cases of positive selection will turn out to involve the fixation of slightly deleterious mutations by genetic drift in bottlenecked populations. Slightly deleterious variants are a transient feature of evolution in the long term, but they have substantially affected contemporary species, including our own.

Comparative analysis of testis protein evolution in rodents

Genes expressed in testes are critical to male reproductive success, affecting spermatogenesis, sperm competition, and sperm-egg interaction. Comparing the evolution of testis proteins at different taxonomic levels can reveal which genes and functional classes are targets of natural and sexual selection and whether the same genes are targets among taxa. Here we examine the evolution of testis-expressed proteins at different levels of divergence among three rodents, mouse (Mus musculus), rat (Rattus norvegicus), and deer mouse (Peromyscus maniculatus), to identify rapidly evolving genes. Comparison of expressed sequence tags (ESTs) from testes suggests that proteins with testis-specific expression evolve more rapidly on average than proteins with maximal expression in other tissues. Genes with the highest rates of evolution have a variety of functional roles including signal transduction, DNA binding, and egg-sperm interaction. Most of these rapidly evolving genes have not been identified previously as targets of selection in comparisons among more divergent mammals. To determine if these genes are evolving rapidly among closely related species, we sequenced 11 of these genes in six Peromyscus species and found evidence for positive selection in five of them. Together, these results demonstrate rapid evolution of functionally diverse testis-expressed proteins in rodents, including the identification of amino acids under lineage-specific selection in Peromyscus. Evidence for positive selection among closely related species suggests that changes in these proteins may have consequences for reproductive isolation.

The evolution of multiple isotypic IgM heavy chain genes in the shark

The IgM H chain gene organization of cartilaginous fishes consists of 15-200 miniloci, each with a few gene segments (V(H)-D1-D2-J(H)) and one C gene. This is a gene arrangement ancestral to the complex IgH locus that exists in all other vertebrate classes. To understand the molecular evolution of this system, we studied the nurse shark, which has relatively fewer loci, and characterized the IgH isotypes for organization, functionality, and the somatic diversification mechanisms that act upon them. Gene numbers differ slightly between individuals ( approximately 15), but five active IgM subclasses are always present. Each gene undergoes rearrangement that is strictly confined within the minilocus; in B cells there is no interaction between adjacent loci located > or =120 kb apart. Without combinatorial events, the shark IgM H chain repertoire is based on junctional diversity and, subsequently, somatic hypermutation. We suggest that the significant contribution by junctional diversification reflects the selected novelty introduced by RAG in the early vertebrate ancestor, whereas combinatorial diversity coevolved with the complex translocon organization. Moreover, unlike other cartilaginous fishes, there are no germline-joined VDJ at any nurse shark mu locus, and we suggest that such genes, when functional, are species-specific and may have specialized roles. With an entire complement of IgM genes available for the first time, phylogenetic analyses were performed to examine how the multiple Ig loci evolved. We found that all domains changed at comparable rates, but V(H) appears to be under strong positive selection for increased amino acid sequence diversity, and surprisingly, so does Cmicro2.

Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes

Using basic probability theory, we show that there is a substantial likelihood that even in the presence of strong purifying selection, there will be a number of codons in which the number of synonymous nucleotide substitutions per site (d (S)) exceeds the number of non-synonymous nucleotide substitutions per site (d (N)). In an empirical study, we examined the numbers of synonymous (b (S)) and non-synonymous substitutions (b (N)) along branches of the phylogenies of 69 single-copy orthologous genes from seven species of mammals. A pattern of b (N) > b (S) was most commonly seen in the shortest branches of the tree and was associated with a high coefficient of variation in both b (N) and b (S), suggesting that high stochastic error in b (N) and b (S) on short branches, rather than positive Darwinian selection, is the explanation of most cases where b (N) is greater than b (S) on a given branch. The branch-site method of Zhang et al. (Zhang, Nielsen, Yang, Mol Biol Evol, 22:2472-2479, 2005) identified 117 codons on 35 branches as "positively selected," but a majority of these codons lacked synonymous substitutions, while in the others, synonymous and non-synonymous differences per site occurred in approximately equal frequencies. Thus, it was impossible to rule out the hypothesis that chance variation in the pattern of mutation across sites, rather than positive selection, accounted for the observed pattern. Our results showed that b (N)/b (S) was consistently elevated in immune system genes, but neither the search for branches with b (N) > b (S) nor the branch-site method revealed this trend.

Frequent and widespread parallel evolution of protein sequences

Understanding the patterns and causes of protein sequence evolution is a major challenge in evolutionary biology. One of the critical unresolved issues is the relative contribution of selection and genetic drift to the fixation of amino acid sequence differences between species. Molecular homoplasy, the independent evolution of the same amino acids at orthologous sites in different taxa, is one potential signature of selection; however, relatively little is known about its prevalence in eukaryotic proteomes. To quantify the extent and type of homoplasy among evolving proteins, we used phylogenetic methodology to analyze 8 genome-scale data matrices from clades of different evolutionary depths that span the eukaryotic tree of life. We found that the frequency of homoplastic amino acid substitutions in eukaryotic proteins was more than 2-fold higher than expected under neutral models of protein evolution. The overwhelming majority of homoplastic substitutions were parallelisms that involved the most frequently exchanged amino acids with similar physicochemical properties and that could be reached by a single-mutational step. We conclude that the role of homoplasy in shaping the protein record is much larger than generally assumed, and we suggest that its high frequency can be explained by both weak positive selection for certain substitutions and purifying selection that constrains substitutions to a small number of functionally equivalent amino acids.

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.

Comparing patterns of natural selection across species using selective signatures

Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 γ-proteobacterial species. We describe the pattern of fast or slow evolution across species as the “selective signature” of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell.

Natural selection promotes the survival of the fittest individuals within a species. Over many generations, this may result in the maintenance of ancestral traits (conservation through purifying selection), or the emergence of newly beneficial traits (adaptation through positive selection). At the genetic level, long-term purifying or positive selection can cause genes to evolve more slowly, or more rapidly, providing a way to identify these evolutionary forces. While some genes are subject to consistent purifying or positive selection in most species, other genes show unexpected levels of selection in a particular species or group of species—a pattern we refer to as the “selective signature” of the gene. In this work, we demonstrate that these patterns of natural selection can be mined for information about gene function and species ecology. In the future, this method could be applied to any set of related species with fully sequenced genomes to better understand the genetic basis of ecological divergence.

Reproductive protein evolution within and between species: maintenance of divergent ZP3 alleles in Peromyscus

In a variety of animal taxa, proteins involved in reproduction evolve more rapidly than nonreproductive proteins. Most studies of reproductive protein evolution, however, focus on divergence between species, and little is known about differentiation among populations within a species. Here we investigate the molecular population genetics of the protein ZP3 within two Peromyscus species. ZP3 is an egg coat protein involved in primary binding of egg and sperm and is essential for fertilization. We find that amino acid polymorphism in the sperm-combining region of ZP3 is high relative to silent polymorphism in both species of Peromyscus. In addition, while there is geographical structure at a mitochondrial gene (Cytb), a nuclear gene (Lcat) and eight microsatellite loci, we find no evidence for geographical structure at Zp3 in Peromyscus truei. These patterns are consistent with the maintenance of ZP3 alleles by balancing selection, possibly due to sexual conflict or pathogen resistance. However, we do not find evidence that reinforcement promotes ZP3 diversification; allelic variation in P. truei is similar among populations, including populations allopatric and sympatric with sibling species. In fact, most alleles are present in all populations sampled across P. truei's range. While additional data are needed to identify the precise evolutionary forces responsible for sequence variation in ZP3, our results suggest that in Peromyscus, selection to maintain divergent alleles within species contributes to the pattern of rapid amino acid substitution observed among species.

Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites

Background

The partitioning of ancestral functions among duplicated genes by neutral evolution, or subfunctionalization, has been considered the primary process for the evolution of novel proteins (neofunctionalization). Nonetheless, how a subfunctionalized protein can evolve into a more adaptive protein is poorly understood, mainly due to the limitations of current analytical methods, which can detect only strong selection for amino acid substitutions involved in adaptive molecular evolution. In this study, we employed a comparative evolutionary approach to this question, focusing on differences in the structural properties of a protein, specifically the electric charge, encoded by fish-specific duplicated phosphoglucose isomerase (Pgi) genes.

Results

Full-length cDNA cloning, RT-PCR based gene expression analyses, and comparative sequence analyses showed that after subfunctionalization with respect to the expression organ of duplicate Pgi genes, the net electric charge of the PGI-1 protein expressed mainly in internal tissues became more negative, and that of PGI-2 expressed mainly in muscular tissues became more positive. The difference in net protein charge was attributable not to specific amino acid sites but to the sum of various amino acid sites located on the surface of the PGI molecule.

Conclusion

This finding suggests that the surface charge evolution of PGI proteins was not driven by strong selection on individual amino acid sites leading to permanent fixation of a particular residue, but rather was driven by weak selection on a large number of amino acid sites and consequently by steady directional and/or purifying selection on the overall structural properties of the protein, which is derived from many modifiable sites. The mode of molecular evolution presented here may be relevant to various cases of adaptive modification in proteins, such as hydrophobic properties, molecular size, and electric charge.